If I have a predicted sequence for a protein and I want to find where it is located on a genome and find other similar sequences to it on the genome, how would I go about doing this and which tools would be best for this task?
If we are talking about organisms without introns, it is very simple. A tool to use is tblastn which can be accessed from the main BLAST page. You can download the BLAST package and run the search locally. There are many other sequence search programs such as DIAMOND that can perform the same type of analysis.
It is more complicated for organisms with discontinuous genes, but it is the same general principle.